FASTQ Sequence and Sequence Quality Format
Countries that developed this resource United Kingdom
Created in 2008
How to cite this record FAIRsharing.org: FASTQ Sequence and Sequence Quality Format; FASTQ Sequence and Sequence Quality Format; DOI: https://doi.org/10.25504/FAIRsharing.r2ts5t; Last edited: April 27, 2021, 8:02 a.m.; Last accessed: Oct 24 2021 10:05 a.m.
Record updated: April 16, 2021, 5:29 p.m. by The FAIRsharing Team.
Edits to 'https://fairsharing.org/FAIRsharing.r2ts5t' by 'The FAIRsharing Team' at 17:29, 16 Apr 2021 (approved): 'organizations' has been modified: Before: Biotechnology and Biological Sciences Research Council (BBSRC), UK|https://bbsrc.ukri.org|Funds European Commission under FP7 Grant Agreement|http://ec.europa.eu/research/fp7/index_en.cfm?pg=documents|Undefined The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK|http://www.sanger.ac.uk|Maintains After: Biotechnology and Biological Sciences Research Council (BBSRC), UK|https://bbsrc.ukri.org|Funds The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK|http://www.sanger.ac.uk|Maintains European Commission under FP7 Grant Agreement|http://ec.europa.eu/research/fp7/index_en.cfm?pg=documents|Funds Added: European Commission under FP7 Grant Agreement|http://ec.europa.eu/research/fp7/index_en.cfm?pg=documents|Funds Removed: European Commission under FP7 Grant Agreement|http://ec.europa.eu/research/fp7/index_en.cfm?pg=documents|Undefined
Edits to 'https://fairsharing.org/FAIRsharing.r2ts5t' by 'The FAIRsharing Team' at 10:02, 21 Nov 2018 (approved): 'domains' has been modified: Before: Deoxyribonucleic acid (DNA) Experimental measurement Life Science After: Amino acid sequence Deoxyribonucleic acid (DNA) Experimental measurement Life Science Added: Amino acid sequence Removed: 'miriam_id' has been modified: Before: None After:
Edits to 'https://fairsharing.org/FAIRsharing.r2ts5t' by 'The FAIRsharing Team' at 22:14, 18 Oct 2016 (approved): 'description' has been modified: Before: "FASTQ Sequence and Sequence Quality Format" is a standard, specialising in the fields described under "scope and data types", below. Until this entry is claimed, more information on this project can be found at http://news.open-bio.org/news/2009/12/nar-fastq-format/. This text was generated automatically. If you work on the project responsible for "FASTQ Sequence and Sequence Quality Format" then please consider helping us by claiming this record and updating it appropriately. After: FASTQ is a text-based file format for sharing sequencing data combining both the sequence and an associated per base quality score. Countries have changed: Previous values: New values: United Kingdom Domain list has changed: Previous values: DNA|material|http://purl.org/obo/owl/GO#GO_0005574 Protein sequence data|property|http://purl.obolibrary.org/obo/ERO_0000084 Quality measure|property| New values: DNA|material|http://purl.org/obo/owl/GO#GO_0005574 Protein sequence data|property|http://purl.obolibrary.org/obo/ERO_0000084 Quality measure|property| Life Science|domain| Taxonomy list has changed: Previous values: New values: All|http://identifiers.org/taxonomy/1?resource=MIR:00100019 Publication List has changed: Previous values: New values: The Sanger FASTQ file format for sequences with quality scores|and the Solexa/Illumina FASTQ variants. Organisations have changed: Previous values: New values: The Wellcome Trust Sanger Institute European Bioinformatics Institute (EMBL-EBI)|Wellcome Trust Genome Campus|Hinxton|Cambridge|UK Grants have changed: Previous values: New values: BBR/G02264X/1 BB/D018358/1
No XSD schemas defined
Conditions of Use
No semantic standards defined
Models and Formats
No identifier schema standards defined
No metrics standards defined
GenBank is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences. The complete release notes for the current version of GenBank are available on the NCBI ftp site. A new release is made every two months. GenBank growth statistics for both the traditional GenBank divisions and the WGS division are available from each release. GenBank is part of the International Nucleotide Sequence Database Collaboration (INSDC), which comprises the DNA DataBank of Japan (DDBJ), the European Molecular Biology Laboratory (EMBL), and GenBank at the NCBI. These three organizations exchange data on a daily basis.
Aspergillus Genome Database
The Aspergillus Genome Database is a resource for genomic sequence data as well as gene and protein information for Aspergilli. This publicly available repository is a central point of access to genome, transcriptome and polymorphism data for the fungal research community.
DNA Data Bank of Japan
An annotated collection of all publicly available nucleotide and protein sequences. DDBJ collects sequence data mainly from Japanese researchers, as well as researchers in other countries. DDBJ is part of the International Nucleotide Sequence Database Collaboration (INSDC), which comprises the DNA DataBank of Japan (DDBJ), the European Molecular Biology Laboratory (EMBL), and GenBank at the NCBI. These three organizations exchange data on a daily basis.
Encyclopedia of DNA Elements at UCSC
Encyclopedia of DNA Elements (ENCODE) has created a comprehensive parts list of functional elements in the human genome, including elements that act at the protein and RNA levels, and regulatory elements that control cells and circumstances in which a gene is active. UCSC coordinated data for the ENCODE Consortium from its inception in 2003 (Pilot phase) to the end of the first 5 year phase of whole-genome data production in 2012. All data produced by ENCODE investigators and the results of ENCODE analysis projects from this period are hosted in the UCSC Genome browser and database.
Integrated Microbial Genomes And Microbiomes
The Integrated Microbial Genomes (IMG/M) aims to support the annotation, analysis and distribution of microbial genome and microbiome datasets sequenced at DOE's Joint Genome Institute (JGI). It also serves as a community resource for analysis and annotation of genome and metagenome datasets in a comprehensive comparative context. The IMG data warehouse integrates genome and metagenome datasets provided by IMG users with a set of publicly available genome and metagenome datasets. IMG/M is also open to scientists worldwide for the annotation, analysis, and distribution of their own genome and microbiome datasets, as long as they agree with the IMG/M data release policy and follow the metadata requirements for integrating data into IMG/M.
modMine is an integrated web resource of data and tools to browse and search modENCODE data and experimental details, download results and access the GBrowse genome browser.
A comprehensive online knowledgebase for the monkey research community.
Mammalian Protein Localization Database
LOCATE is a curated database that houses data describing the membrane organization and subcellular localization of proteins from the RIKEN FANTOM4 mouse and human protein sequence set.
Endocrine Pancreas Consortium Database
EPConDB is a resource of the Beta Cell Biology Consortium which displays information about genes expressed in cells of the pancreas and their transcriptional regulation.
Bgee DataBase for Gene Expression Evolution
Bgee is a database to retrieve and compare gene expression patterns in multiple animal species, produced from multiple data types (RNA-Seq, Affymetrix, in situ hybridization, and EST data). Bgee is based exclusively on curated "normal", healthy, expression data (e.g., no gene knock-out, no treatment, no disease), to provide a comparable reference of normal gene expression. Bgee produces calls of presence/absence of expression, and of differential over-/under-expression, integrated along with information of gene orthology, and of homology between organs. This allows comparisons of expression patterns between species.
Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants
Gramene's purpose is to provide added value to plant genomics data sets available within the public sector, which will facilitate researchers' ability to understand the plant genomes and take advantage of genomic sequence known in one species for identifying and understanding corresponding genes, pathways and phenotypes in other plant species. It represents a broad spectrum of species ranging from unicellular photo-autotrophs, algae, monocots, dicots and other important taxonomic clades. Within Plant Reactome, a database portal of Gramene, there are over 60 plant genomes as well as pathways for more than 80 species.
European Nucleotide Archive
The European Nucleotide Archive (ENA) is a globally comprehensive data resource for nucleotide sequence, spanning raw data, alignments and assemblies, functional and taxonomic annotation and rich contextual data relating to sequenced samples and experimental design. Serving both as the database of record for the output of the world's sequencing activity and as a platform for the management, sharing and publication of sequence data, the ENA provides a portfolio of services for submission, data management, search and retrieval across web and programmatic interfaces. The ENA is part of the International Nucleotide Sequence Database Collaboration (INSDC), which comprises the DNA DataBank of Japan (DDBJ), the European Molecular Biology Laboratory (EMBL), and GenBank at the NCBI. These three organizations exchange data on a daily basis.
The European Genome-phenome Archive
The European Genome-phenome Archive (EGA) allows you to explore datasets from genomic studies, provided by a range of data providers. Access to datasets must be approved by the specified Data Access Committee (DAC).
EBI Metagenomics has changed its name to MGnify to reflect a change in scope. This is a free-to-use resource aiming at supporting all metagenomics researchers. The service is an automated pipeline for the analysis and archiving of metagenomic data that aims to provide insights into the phylogenetic diversity as well as the functional and metabolic potential of a sample. You can freely browse all the public data in the repository.
The ENCODE (Encyclopedia of DNA Elements) Consortium is an international collaboration of research groups funded by the National Human Genome Research Institute (NHGRI). The goal of ENCODE is to build a comprehensive parts list of functional elements in the human genome, including elements that act at the protein and RNA levels, and regulatory elements that control cells and circumstances in which a gene is active. ENCODE results from 2007 and later are available from this project. This covers data generated during the two production phases 2007-2012 and 2013-present.
Dog Genome SNP Database
Dog Genome SNP Database (DoGSD) is a data container for the variation information of dog/wolf genomes. It was designed and constructed as an SNPs detector and visualization tool to provide the research community a useful resource for the study of dog's population, evolution, phenotype and life habit.
Genome Sequence Archive
GSA is a data repository specialized for archiving raw sequence reads. It supports data generated from a variety of sequencing platforms ranging from Sanger sequencing machines to single-cell sequencing machines and provides data storing and sharing services free of charge for worldwide scientific communities. In addition to raw sequencing data, GSA also accommodates secondary analyzed files in acceptable formats (like BAM, VCF). Its user-friendly web interfaces simplify data entry and submitted data are roughly organized as two parts, viz., Metadata and File, where the former can be further assorted into BioProject, BioSample, Experiment and Run, and the latter contains raw sequence reads.
4DNucleome Data Portal
The 4D Nucleome Data Portal (4DN) hosts data generated by the 4DN Network and other reference nucleomics data sets, and an expanding tool set for open data processing and visualization. It is a platform to search, visualize, and download nucleomics data.
Sorghum Genome SNP Database
The Sorghum Genome SNP Database (SorGSD) is a genome variation database for sorghum. Please note that this resource has not been updated since 2015, and therefore we have marked its status as Uncertain. Please contact us if you have information on its current status.
National Cancer Institute's Genomic Data Commons
The National Cancer Institute’s (NCI’s) Genomic Data Commons (GDC) is a data sharing The National Cancer Institute's Genomic Data Commons (GDC) was created to promote precision medicine in oncology. It supports the import and standardization of genomic and clinical data from cancer research programs. The GDC contains NCI-generated data from some of the largest and most comprehensive cancer genomic datasets, including The Cancer Genome Atlas (TCGA) and Therapeutically Applicable Research to Generate Effective Therapies (TARGET). For the first time, these datasets have been harmonized using a common set of bioinformatics pipelines, so that the data can be directly compared. As a growing knowledge system for cancer, the GDC also enables researchers to submit data, and harmonizes these data for import into the GDC.
DDBJ Sequence Read Archive
DDBJ Sequence Read Archive (DRA) is an archive database for output data generated by next-generation sequencing machines including Roche 454 GS System®, Illumina Genome Analyzer®, Applied Biosystems SOLiD® System, and others. DRA is a member of the International Nucleotide Sequence Database Collaboration (INSDC) and archiving the data in a close collaboration with NCBI Sequence Read Archive (SRA) and EBI Sequence Read Archive (ERA).
Genomic Observatories Meta-Database
The Genomic Observatories Meta-Database (GEOME) is a web-based database that captures the who, what, where, and when of biological samples and associated genetic sequences. GEOME helps users with the following goals: ensure the metadata from your biological samples is findable, accessible, interoperable, and reusable; improve the quality of your data and comply with global data standards; and integrate with R, ease publication to NCBI's sequence read archive, and work with an associated LIMS. The initial use case for GEOME came from the Diversity of the Indo-Pacific Network (DIPnet) resource.
Scroll for more...
This record is not implemented by any policy.
This record is in need of a maintainer. If you login, you'll be able to claim this record.
Biotechnology and Biological Sciences Research Council (BBSRC), UK (Government body)
European Commission under FP7 Grant Agreement (Government body)
BB/D018358/1 (Biotechnology and Biological Sciences Research Council (BBSRC), UK)
BBR/G02264X/1 (Biotechnology and Biological Sciences Research Council (BBSRC), UK)